It seems this is the BioC package affxparser. So my suggestion does work with
R CMD INSTALL affxparser and using the preferred form of OBJECTS instead of OBJS also works. BDR On Thu, 12 Jul 2007, Prof Brian Ripley wrote: > You seem extraordinarily reluctant to tell us what you are actually doing: no > command appears here. I presume this is a call to R CMD INSTALL, but why do > I have to keep guessing? > > Since you have taken over the make action via the all: target in your > Makevars, you need also to take over responsibility for cleaning. I should > think > > all: myclean $(SHLIB) > > myclean: > rm -f $(OBJS) > > should do it. And BTW, the use of $(OBJS) to set the objects is > undocumented, at least in 'Writing R Extensions'. > > On Wed, 11 Jul 2007, Kasper Daniel Hansen wrote: > >> >> On Jul 11, 2007, at 9:30 AM, Prof Brian Ripley wrote: >> >>> On Mon, 9 Jul 2007, Kasper Daniel Hansen wrote: >>> >>>> Hi >>>> >>>> This is a question prompted by the mac version of R, but as I see it, >>>> it should have broader interest. >>>> >>>> These days the CRAN Mac binary per default compiles every package for >>>> two architectures. First i386 and then ppc. In between the two >>>> compilation runs, any object files in pkgname/src is removed. This >>>> cleanup is necessary since otherwise Make would not recompile the >>>> object files under the next architecture. >>>> >>>> I have a package which includes a large SDK which I have put in >>>> src/fusion_sdk >>>> (and subdirectories). I take care of that by using a Makevars file >>>> with essentially (the whole Makevars file is reproduced below) >>>> >>>> PKG_SOURCES = \ >>>> fusion_sdk/calvin_files/data/src/CDFData.cpp >>>> >>>> OBJS=$(PKG_SOURCES:.cpp=.o) >>>> >>>> all: $(SHLIB) >>>> >>>> However, this setup does not remove the object files in the >>>> fusion_sdk subdirectory. From a posting on R-sig-mac by Simon Urbanek >>>> I learned that I need to clean up these directories myself. >>>> >>>> I have - per R extensions - attempted to do so using a pkgname/ >>>> cleanup script. While this works for cleaning up the sub directories >>>> when I do R CMD build, it seems as if this script is not being run >>>> between compilation runs (is this intentional btw.?). >>> >>> What do you mean by 'compilation runs'? The 'cleanup' script will be run >>> by R CMD INSTALL --cleanup (and without --cleanup it is intentionally not >>> run). >>> >>>> So my question is now: how do I in a simple way clean up my >>>> subdirectories? I would prefer it to be as simple as possible because >>>> so far I have not really needed anything besides a Makevars file. In >>>> fact the impression I have right now from looking at the SHLIB and >>>> INSTALL scripts is that I might need a Makefile that removes the >>>> object files _before_ starting the compilation, as I don't really see >>>> any cleanup process (eg. making a target clean) - but this may very >>>> well be due to my limited understanding of these scripts. >>> >>> I see R CMD INSTALL --clean that runs a clean up afterwards, and 2.6.0 >>> will also have R CMD INSTALL --preclean in case you forgot --clean on the >>> last run. >>> >>>> Any help/hints on how to proceed? Especially if I want it to be >>>> portable? >>> >>> What does R CMD INSTALL --clean not do that you want? >>> >>> If you are talking about R CMD SHLIB, that currently does not clean up but >>> this has been raised and it will most likely have a --clean option in >>> 2.6.0 that removes $(OBJECTS). >> >> Perhaps I was not clear enough: The CRAN binary of R for Mac has two >> architectures inside $R_HOME/bin/exec, namely "ppc" and "i386". This means >> that whenever anyone installs a source package I see two compilation runs - >> the following is a shortened output: >> >> * Installing to library '/Library/Frameworks/R.framework/Resources/library' >> * Installing *source* package 'affxparser' ... >> ** libs >> ** arch - i386 >> g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk >> -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/i386 -imacros >> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src >> -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src >> -Ifusion_sdk/calvin_files/fusion/src >> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter >> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter >> -Ifusion_sdk/calvin_files/parameter/src >> -Ifusion_sdk/calvin_files/parsers/src >> -Ifusion_sdk/calvin_files/portability/src >> -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src >> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file >> -Ifusion_sdk/portability -D_USE_MEM_MAPPING_ -msse3 -fPIC -g -O2 -Wall >> -O0 -c fusion_sdk/calvin_files/data/src/CDFData.cpp -o >> fusion_sdk/calvin_files/data/src/CDFData.o >> >> (Now a lot of other files gets compiled) >> >> g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib >> -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module >> -multiply_defined suppress -L/usr/local/lib -o affxparser.so >> fusion_sdk/calvin_files/data/src/CDFData.o >> fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.o >> fusion_sdk/calvin_files/data/src/CDFProbeInformation.o >> fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.o >> fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.o >> fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.o >> fusion_sdk/calvin_files/data/src/CELData.o >> fusion_sdk/calvin_files/data/src/DataGroup.o >> fusion_sdk/calvin_files/data/src/DataGroupHeader.o >> fusion_sdk/calvin_files/data/src/DataSet.o >> fusion_sdk/calvin_files/data/src/DataSetHeader.o >> fusion_sdk/calvin_files/data/src/FileHeader.o >> fusion_sdk/calvin_files/data/src/GenericData.o >> fusion_sdk/calvin_files/data/src/GenericDataHeader.o >> fusion_sdk/calvin_files/exception/src/ExceptionBase.o >> fusion_sdk/calvin_files/fusion/src/CalvinAdapter/CalvinCELDataAdapter.o >> fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.o >> fusion_sdk/calvin_files/fusion/src/FusionCDFData.o >> fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.o >> fusion_sdk/calvin_files/fusion/src/FusionCELData.o >> fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.o >> fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.o >> fusion_sdk/calvin_files/parsers/src/CDFFileReader.o >> fusion_sdk/calvin_files/parsers/src/CelFileReader.o >> fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.o >> fusion_sdk/calvin_files/parsers/src/DataGroupReader.o >> fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.o >> fusion_sdk/calvin_files/parsers/src/DataSetReader.o >> fusion_sdk/calvin_files/parsers/src/FileHeaderReader.o >> fusion_sdk/calvin_files/parsers/src/FileInput.o >> fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.o >> fusion_sdk/calvin_files/parsers/src/GenericFileReader.o >> fusion_sdk/calvin_files/utils/src/AffymetrixGuid.o >> fusion_sdk/calvin_files/utils/src/DateTime.o >> fusion_sdk/calvin_files/utils/src/FileUtils.o >> fusion_sdk/calvin_files/utils/src/StringUtils.o >> fusion_sdk/calvin_files/utils/src/checksum.o >> fusion_sdk/file/BPMAPFileData.o fusion_sdk/file/BPMAPFileWriter.o >> fusion_sdk/file/CDFFileData.o fusion_sdk/file/CELFileData.o >> fusion_sdk/file/FileIO.o fusion_sdk/file/FileWriter.o R_affx_cel_parser.o >> R_affx_cdf_parser.o R_affx_cdf_extras.o R_affx_bpmap_parser.o >> -F/Library/Frameworks/R.framework/.. -framework R >> ** arch - ppc >> g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp >> -I/Library/Frameworks/R.framework/Resources/include >> -I/Library/Frameworks/R.framework/Resources/include/ppc -imacros >> R_affx_constants.h -Ifusion_sdk/calvin_files/array/src >> -Ifusion_sdk/calvin_files/data/src -Ifusion_sdk/calvin_files/exception/src >> -Ifusion_sdk/calvin_files/fusion/src >> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter >> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter >> -Ifusion_sdk/calvin_files/parameter/src >> -Ifusion_sdk/calvin_files/parsers/src >> -Ifusion_sdk/calvin_files/portability/src >> -Ifusion_sdk/calvin_files/template/src -Ifusion_sdk/calvin_files/utils/src >> -Ifusion_sdk/calvin_files/writers/src -Ifusion_sdk/file >> -Ifusion_sdk/portability -D_USE_MEM_MAPPING_ -I/usr/local/include -fPIC >> -g -O2 -Wall -O0 -c R_affx_cel_parser.cpp -o R_affx_cel_parser.o >> >> As you see from this (and sorry for all the include statements), when R >> starts compiling for arch = "ppc", it starts with a with in /src whereas >> the first compilation run (or more precise the first architecture) starts >> from /src/fusion_sdk/calvin_files/data/src. This is of course because the >> object files in the subdirectories do not get removed between the two >> architectures. >> >> This has - probably - something to do with R CMD SHLIB not cleaning up >> after itself. A method of removing $(OBJECTS) would be exactly what I need, >> and may I suggest that this is done per default instead of being set by an >> option. Anyone using the CRAN binary for the Mac will have the same problem >> as I. >> >> I am happy to see that this may be fixed for R-2.6.0. Is there anything I >> can do in the meantime for getting my package to work under R-2.5.1? (I can >> always move my source files from the /src/fusion_sdk subdirectories >> directly into /src, but I would prefer to avoid that). >> >>>> >>>> Kasper >>>> >>>> The full Makevars file: >>>> >>>> MYCXXFLAGS=-O0 >>> >>> You do realize that is highly non-portable? >> >> Yes, but I do not know of any other way to downgrade the optimization >> level. The SDK I am using breaks (due to memory alignment issues if a >> specific optimization flag for GCC is include - the flag is certainly >> implied by -O2 and as far as I recall also -O1). I guess the solution is to >> switch to an autoconfigure script. The main reason for not doing this is 1) >> time and actually more 2) the fact that the SDK does not come with an ac >> script. >> >> Thanks for the feedback, Kasper >> >> >>>> %.o: %.cpp >>>> $(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) $(MYCXXFLAGS) -c $< -o $@ >>>> >>>> PKG_CPPFLAGS=\ >>>> -imacros R_affx_constants.h\ >>>> -Ifusion_sdk/calvin_files/array/src\ >>>> -Ifusion_sdk/calvin_files/data/src\ >>>> -Ifusion_sdk/calvin_files/exception/src\ >>>> -Ifusion_sdk/calvin_files/fusion/src\ >>>> -Ifusion_sdk/calvin_files/fusion/src/GCOSAdapter\ >>>> -Ifusion_sdk/calvin_files/fusion/src/CalvinAdapter\ >>>> -Ifusion_sdk/calvin_files/parameter/src\ >>>> -Ifusion_sdk/calvin_files/parsers/src\ >>>> -Ifusion_sdk/calvin_files/portability/src\ >>>> -Ifusion_sdk/calvin_files/template/src\ >>>> -Ifusion_sdk/calvin_files/utils/src\ >>>> -Ifusion_sdk/calvin_files/writers/src\ >>>> -Ifusion_sdk/file\ >>>> -Ifusion_sdk/portability\ >>>> -D_USE_MEM_MAPPING_ >>>> >>>> PKG_SOURCES = \ >>>> fusion_sdk/calvin_files/data/src/CDFData.cpp\ >>>> fusion_sdk/calvin_files/data/src/CDFProbeGroupInformation.cpp\ >>>> fusion_sdk/calvin_files/data/src/CDFProbeInformation.cpp\ >>>> fusion_sdk/calvin_files/data/src/CDFProbeSetInformation.cpp\ >>>> fusion_sdk/calvin_files/data/src/CDFQCProbeInformation.cpp\ >>>> fusion_sdk/calvin_files/data/src/CDFQCProbeSetInformation.cpp\ >>>> fusion_sdk/calvin_files/data/src/CELData.cpp\ >>>> fusion_sdk/calvin_files/data/src/DataGroup.cpp\ >>>> fusion_sdk/calvin_files/data/src/DataGroupHeader.cpp\ >>>> fusion_sdk/calvin_files/data/src/DataSet.cpp\ >>>> fusion_sdk/calvin_files/data/src/DataSetHeader.cpp\ >>>> fusion_sdk/calvin_files/data/src/FileHeader.cpp\ >>>> fusion_sdk/calvin_files/data/src/GenericData.cpp\ >>>> fusion_sdk/calvin_files/data/src/GenericDataHeader.cpp\ >>>> fusion_sdk/calvin_files/exception/src/ExceptionBase.cpp\ >>>> fusion_sdk/calvin_files/fusion/src/CalvinAdapter/ >>>> CalvinCELDataAdapter.cpp\ >>>> fusion_sdk/calvin_files/fusion/src/FusionBPMAPData.cpp\ >>>> fusion_sdk/calvin_files/fusion/src/FusionCDFData.cpp\ >>>> fusion_sdk/calvin_files/fusion/src/FusionCDFQCProbeSetNames.cpp\ >>>> fusion_sdk/calvin_files/fusion/src/FusionCELData.cpp\ >>>> fusion_sdk/calvin_files/fusion/src/GCOSAdapter/GCOSCELDataAdapter.cpp\ >>>> fusion_sdk/calvin_files/parameter/src/ParameterNameValueType.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/CDFFileReader.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/CelFileReader.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/DataGroupHeaderReader.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/DataGroupReader.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/DataSetHeaderReader.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/DataSetReader.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/FileHeaderReader.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/FileInput.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/GenericDataHeaderReader.cpp\ >>>> fusion_sdk/calvin_files/parsers/src/GenericFileReader.cpp\ >>>> fusion_sdk/calvin_files/utils/src/AffymetrixGuid.cpp\ >>>> fusion_sdk/calvin_files/utils/src/DateTime.cpp\ >>>> fusion_sdk/calvin_files/utils/src/FileUtils.cpp\ >>>> fusion_sdk/calvin_files/utils/src/StringUtils.cpp\ >>>> fusion_sdk/calvin_files/utils/src/checksum.cpp\ >>>> fusion_sdk/file/BPMAPFileData.cpp\ >>>> fusion_sdk/file/BPMAPFileWriter.cpp\ >>>> fusion_sdk/file/CDFFileData.cpp\ >>>> fusion_sdk/file/CELFileData.cpp\ >>>> fusion_sdk/file/FileIO.cpp\ >>>> fusion_sdk/file/FileWriter.cpp\ >>>> R_affx_cel_parser.cpp\ >>>> R_affx_cdf_parser.cpp\ >>>> R_affx_cdf_extras.cpp\ >>>> R_affx_bpmap_parser.cpp >>>> >>>> OBJS=$(PKG_SOURCES:.cpp=.o) >>>> >>>> all: $(SHLIB) >>> >>> -- >>> Brian D. Ripley, [EMAIL PROTECTED] >>> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ >>> University of Oxford, Tel: +44 1865 272861 (self) >>> 1 South Parks Road, +44 1865 272866 (PA) >>> Oxford OX1 3TG, UK Fax: +44 1865 272595 > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
